User: Johannes Rainer

gravatar for Johannes Rainer
Johannes Rainer1.1k
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Italy
Twitter:
@jotsetung
Last seen:
23 hours ago
Joined:
3 years, 2 months ago
Email:
j**************@eurac.edu

PhD, Bioinformatics Group, Institute for Biomedicine, Eurac Research, Bolzano, Italy

 

Posts by Johannes Rainer

<prev • 218 results • page 1 of 22 • next >
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Answer: A: ensembldb and pseudogenes mapping to the same Ensembl ID
... Dear Meeta, mapping between Entrez and Ensembl IDs is always problematic. EnsDb databases provide you with all the information from Ensembl (for a specific release) and in version 79 (March 2015) this one gene was annotated to two Entrez identifiers. Unfortunately, in EnsDb databases, there is no a ...
written 7 days ago by Johannes Rainer1.1k
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Comment: C: error when using ensembldb with a MySQL server
... You need to create a user. Please refer to the mysql documentation for that - you'll find a lot information on the internet how to create a new user in mysql. ...
written 17 days ago by Johannes Rainer1.1k
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Comment: C: error when using ensembldb with a MySQL server
... This sounds like there is a problem connecting to MySQL which is independent of R. Is the MySQL server running? Can you connect using mysql -h localhost -u readonly -p ? or if you use 127.0.0.1 instead of localhost?   ...
written 19 days ago by Johannes Rainer1.1k
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News: Ensembl 91 EnsDb databases added to AnnotationHub
... Dear all, EnsDb databases (for ensembldb) for Ensembl release 91 are available for current Bioc3.7 (devel). > library(AnnotationHub) > query(AnnotationHub(), "Ensembl 91 EnsDb") snapshotDate(): 2017-12-21 AnnotationHub with 88 records # snapshotDate(): 2017-12-21 # $dataprovider: Ensembl # ...
annotation news ensembl ensembldb written 25 days ago by Johannes Rainer1.1k
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Comment: C: Error : object path is not exported by namespace:Rsamtools
... Thanks for reporting! I'll look into it. ...
written 29 days ago by Johannes Rainer1.1k
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News: Map between protein and genome coordinates using ensembldb
... ensembldb version 2.3.2 (Bioconductor developmental version) provides functions to map between genomic, transcript and protein coordinates. Check the coordinate-mapping vignette! ...
annotation news ensembdb written 6 weeks ago by Johannes Rainer1.1k
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Comment: C: How to create tx2gene data.frame when there's no TxDb object for the organism yo
... Might be a problem in the makeTxDbFromGFF function from the GenomicFeatures package. It works with the ensDbFromGtf from the ensembldb package. > library(ensembldb) > dbf <- ensDbFromGtf("Oryza_sativa.IRGSP-1.0.37.gtf.gz") Importing GTF file ... OK Processing metadata ... OK Processing ge ...
written 7 weeks ago by Johannes Rainer1.1k
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Comment: C: Is it possible to annotated mitochondrial genes with ENSEMBL ids and Homo.sapien
... Just to avoid confusion: AnnotationHub is a central repository for annotation resources. AnnotationHub contains many different databases among those EnsDb databases, TxDb databases, genomic sequences etc. I wouldn't call them AH#### databases, the AH#### is just the ID of the resource in AnnotationH ...
written 7 weeks ago by Johannes Rainer1.1k
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Answer: A: Is it possible to annotated mitochondrial genes with ENSEMBL ids and Homo.sapien
... Regarding annotations of mitochondrial genes - if you're interested in Ensembl IDs (or have Ensembl gene IDs) you might give ensembldb and EnsDb databases a try. You can fetch mitochondrial genes from an EnsDb: > library(EnsDb.Hsapiens.v75) > gns <- genes(EnsDb.Hsapiens.v75, filter = ~ se ...
written 8 weeks ago by Johannes Rainer1.1k
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Answer: A: ReadMSData problem with xcms
... readMSData with mode = "inMem" (the default) will by default read only MS level >= 2 from the input files. If you are going to use xcms you should use readMSData(temp, pdata = pheno, mode = "onDisk") which will a) read all MS levels from the input file and b) return a OnDiskMSnExp object that you ...
written 8 weeks ago by Johannes Rainer1.1k

Latest awards to Johannes Rainer

Scholar 7 months ago, created an answer that has been accepted. For A: annotating gene for transcript type/biotype
Great Question 7 months ago, created a question with more than 5,000 views. For Problem with biomart's listMarts function
Student 8 months ago, asked a question with at least 3 up-votes. For Easy way to sort GRangesList by seqname/start position?
Student 9 months ago, asked a question with at least 3 up-votes. For Problem with biomart's listMarts function
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Problem running dexseq in parallel using BiocParallel
Scholar 9 months ago, created an answer that has been accepted. For A: annotating gene for transcript type/biotype
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: makeTxDbFromBiomart Error: 1: Space required after the Public Identifier
Teacher 21 months ago, created an answer with at least 3 up-votes. For A: biomaRt no longer works with proxy after upgrade
Scholar 21 months ago, created an answer that has been accepted. For A: Missing SYMBOL keytype in EnsDb.Hsapiens.v75
Scholar 21 months ago, created an answer that has been accepted. For A: ensembldb: ensDbFromGtf error with ensembl version 74
Scholar 21 months ago, created an answer that has been accepted. For A: biomaRt no longer works with proxy after upgrade
Scholar 21 months ago, created an answer that has been accepted. For A: biomaRt package problem
Scholar 21 months ago, created an answer that has been accepted. For A: annotating gene for transcript type/biotype
Popular Question 23 months ago, created a question with more than 1,000 views. For Problem with biomart's listMarts function
Appreciated 2.0 years ago, created a post with more than 5 votes. For A: biomaRt no longer works with proxy after upgrade
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: makeTxDbFromBiomart Error: 1: Space required after the Public Identifier
Centurion 2.1 years ago, created 100 posts.
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: biomaRt no longer works with proxy after upgrade
Scholar 2.2 years ago, created an answer that has been accepted. For A: annotating gene for transcript type/biotype
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: biomaRt no longer works with proxy after upgrade
Scholar 2.2 years ago, created an answer that has been accepted. For A: annotating gene for transcript type/biotype
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Scholar 2.2 years ago, created an answer that has been accepted. For A: annotating gene for transcript type/biotype
Autobiographer 2.6 years ago, has more than 80 characters in the information field of the user's profile.

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